Added the program for April 2014.

misc/Makefile

+# Makefile for LaTeX documents.
+#
+
+# LaTeX core binaries.
+TEX := latex
+BIBTEX := bibtex
+GLOSSARY := makeglossaries
+
+# Conversion to other formats.
+DVIPS := dvips
+PS2PDF := ps2pdf14
+LATEX2RTF := latex2rtf
+LIBREOFFICE := libreoffice
+
+# Pictures.
+DIA := dia
+CONVERT := convert
+GNUPLOT := gnuplot
+FONTSIZE := 20
+
+# Load the configuration file.
+-include config.mkc
+
+# Find the input files.
+SRC := $(basename $(shell grep -l '\\begin{document}' *.tex))
+PIC := $(basename $(shell ls *.dia))
+GNP := $(basename $(shell ls *.gnp))
+
+# Output.
+PDF := $(addsuffix .pdf, $(SRC))
+RTF := $(addsuffix .rtf, $(SRC))
+DOC := $(addsuffix .docx, $(SRC))
+
+# Temporary files.
+TMP := blg log nav out snm toc dvi aux idx vrb ps glg glo ist
+PNG := $(addsuffix .png, $(PIC))
+TNP := $(addsuffix .tnp, $(GNP))
+
+# Semi-permanent files.
+BIB := $(addsuffix .bbl, $(SRC))
+GLS := $(addsuffix .gls, $(GLS))
+EPS := $(addsuffix .eps, $(PIC) $(GNP))
+
+# Do not delete the semi-permanent files automatically.
+.PRECIOUS: $(BIB) $(GLS) $(EPS)
+
+# Disable built-in rules.
+.SUFFIXES:
+
+# Targets that are not associated with files.
+.PHONY: all rtf doc clean distclean release
+
+
+# Main targets
+
+all: $(PDF)
+
+rtf: $(RTF)
+
+doc: $(DOC)
+
+clean:
+	rm -f $(foreach I, $(TMP), $(addsuffix .$I, $(SRC))) $(PNG) $(TNP)
+
+distclean: clean
+	rm -f $(PDF) $(RTF) $(DOC) $(BIB) $(EPS)
+
+release: all clean
+
+
+# Picture targets.
+
+%.png: %.dia
+	$(DIA) -e $@ -t png-libart $<
+
+%.eps: %.png
+	$(CONVERT) $< $@
+
+%.tnp: %.gnp $(DEP)
+	echo "set terminal postscript color eps font \"default,$(FONTSIZE)\"" > $@ ;\
+	cat $< >> $@
+
+%.eps: %.tnp
+	$(GNUPLOT) < $< > $@
+
+
+# BibTeX targets (called recursively).
+
+%.blg: %.aux
+	$(BIBTEX) $(basename $^)
+
+%.bbl: %.blg
+	@
+
+# Glossary targets (called recursively).
+
+%.glg: %.aux
+	$(GLOSSARY) $*
+
+%.glo: %.glg
+	@
+
+%.ist: %.glg
+	@
+
+%.gls: %.aux %.glg %.glo %.ist
+	@
+
+# LaTeX build targets.
+
+%.aux: %.tex $(EPS)
+	$(TEX) $< ;\
+	if (grep -s "LaTeX Warning: Citation" $*.log); then \
+	  $(MAKE) $*.bbl ;\
+	  $(TEX) $< ;\
+	fi ;\
+	if (grep -s "No file $*.gls" $*.log); then \
+	  $(MAKE) $*.gls ;\
+	fi ;\
+	while (grep -s "Rerun to get cross-references right." $*.log); do \
+	  $(TEX) $< ;\
+	done ;\
+	while (grep -s "LaTeX Warning: There were undefined references" $*.log); do \
+	  $(TEX) $< ;\
+	done ;\
+	while (grep -s "Package rerunfilecheck Warning: File" $*.log); do \
+	  $(TEX) $< ;\
+	done
+
+%.log: %.aux
+	@
+
+%.dvi: %.aux
+	@
+
+%.idx: %.aux
+	@
+
+%.nav: %.aux
+	@
+
+%.out: %.aux
+	@
+
+%.snm: %.aux
+	@
+
+%.toc: %.aux
+	@
+
+%.vrb: %.aux
+	@
+
+%.ps: %.dvi %.log %.aux %.idx %.nav %.out %.snm %.toc %.vrb
+	$(DVIPS) $< -o $@
+
+
+# Output targets.
+
+%.pdf: %.ps
+	$(PS2PDF) $^
+
+%.rtf: %.tex %.dvi %.log %.aux %.idx %.nav %.out %.snm %.toc %.vrb
+	$(LATEX2RTF) -o $@ $<
+
+%.docx: %.rtf
+	$(LIBREOFFICE) --headless --invisible --convert-to docx $< -o $@

program/Makefile

+../misc/Makefile
\ No newline at end of file

program/local.sty

+% One space after a period.
+\frenchspacing
+
+% Squeeze the itemisation lists.
+\let\tempitemize=\itemize
+\renewcommand\itemize{
+  \vspace{-0.25\baselineskip}
+  \tempitemize
+  \setlength{\itemsep}{0pt}
+}
+\let\tempenditemize=\enditemize
+\renewcommand\enditemize{
+  \tempenditemize
+  \vspace{-0.25\baselineskip}
+}
+
+% Squeeze the enumeration lists.
+\let\tempenumerate=\enumerate
+\renewcommand\enumerate{
+  \vspace{-0.25\baselineskip}
+  \tempenumerate
+  \setlength{\itemsep}{0pt}
+}
+\let\tempendenumerate=\endenumerate
+\renewcommand\endenumerate{
+  \tempendenumerate
+  \vspace{-0.25\baselineskip}
+}

program/program.tex

+\documentclass{article}
+\usepackage{fullpage}
+
+\usepackage{local}
+
+\providecommand{\personOne}{Jeroen Laros}
+\providecommand{\personTwo}{Michiel van Galen}
+\providecommand{\myDate}{April 1 and 4, 2014}
+\providecommand{\myLocation}{Avans Hogeschool, Breda}
+
+\frenchspacing
+\setlength{\parindent}{0pt}
+\pagestyle{empty}
+
+\begin{document}
+\begin{center}
+LUMC: Human and Clinical Genetics
+
+{\bf NGS Introduction Course}
+
+\myDate
+
+Location: \myLocation
+\bigskip
+
+Given by: \personTwo\ and \personOne.
+\end{center}
+\bigskip
+
+The course aims at introducing participants (with no or little experience) to
+NGS data analysis. The course is split into two parts: in the first session
+we look at the building blocks of NGS pipelines, in the second session we look
+at the general picture.
+\bigskip
+\bigskip
+
+{\bf Program:}
+\bigskip
+
+{\bf Session one:}
+\medskip
+
+\begin{tabular}{r@{\hspace{3pt}}l@{\hspace{2pt}}rp{9cm}l}
+13:30 &-& 13:45 & Introduction to NGS data analysis & \personTwo\\
+13:45 &-& 14:00 & Operating system basics           & \personOne\\
+14:00 &-& 14:30 & Installing and updating software  & \personOne\\
+14:30 &-& 15:00 & Getting started                   & \personTwo\\
+\\
+15:00 &-& 15:30 & Break\\
+\\
+15:30 &-& 16:00 & Connecting to other machines      & \personOne\\
+16:00 &-& 17:30 & Practical\\
+\end{tabular}
+\bigskip
+
+The practical covers the following:
+\begin{itemize}
+  \item Connecting to a remote machine.
+  \item Using the command line.
+  \item Downloading and installing tools.
+  \item Running a simple analysis.
+\end{itemize}
+\bigskip
+\bigskip
+
+{\bf Session two:}
+\medskip
+
+\begin{tabular}{r@{\hspace{3pt}}l@{\hspace{2pt}}rp{9cm}l}
+14:00 &-& 14:30 & Combining tools into a pipeline  & \personTwo\\
+\\
+14:30 &-& 15:00 & Break\\
+\\
+15:00 &-& 16:30 & Practical\\
+\end{tabular}
+\bigskip
+
+The practical covers the following:
+\begin{itemize}
+  \item Making a static shell script.
+  \item Variables.
+  \item Command line arguments.
+  \item Making a dynamic pipeline.
+\end{itemize}
+\end{document}